Responds to reports (including Massey et al.’s reinstated candidates, S-7, and two newer T/T-haplotype genomes surfaced from Shanghai) of genomes that appear intermediate between lineage A and B at the two defining positions. Using phylogenetic placement and the genomes’ full mutational context (not just the two defining sites), the authors argue these genomes are “derived” rather than “intermediate”: each nests phylogenetically inside lineage A or B and carries additional descendant mutations, consistent with recurrent/back-mutation at the two fast-evolving defining sites within an already-established lineage rather than with sampling a true ancestral intermediate that would bridge the two spillovers. If accepted, this closes the specific “reinstated intermediate genomes falsify two introductions” line of attack (S-7); if not, the intermediates stand as evidence for a single introduction with in-lineage recurrent mutation.
relevance_note: the zoonosis side’s direct technical answer to the strongest documented data-exclusion critique of the two-introduction claim — the dispute currently ends here in the published record.